黄瓜DIR家族基因的全基因组鉴定及其表达分析

doi:10.3864/j.issn.0578-1752.2023.04.010

中国农业科学 ›› 2023, Vol. 56 ›› Issue (4): 711-728.doi: 10.3864/j.issn.0578-1752.2023.04.010

黄瓜DIR家族基因的全基因组鉴定及其表达分析

张开京¹(), 何帅帅¹, 贾利², 胡玉超¹, 杨德坤¹, 陆晓民¹, 张其安², 严从生²()

¹安徽科技学院农学院，安徽凤阳 233100
²安徽省农业科学院园艺研究所/农业农村部园艺作物种质创制与利用重点实验室（部省共建）/园艺作物种质创制及生理生态安徽省重点实验室，合肥 230031

收稿日期:2022-04-13 接受日期:2022-06-07 出版日期:2023-02-16 发布日期:2023-02-24
通信作者: 严从生，E-mail：congshengyan@126.com
联系方式: 张开京，E-mail：zhangkj@ahstu.edu.cn。
基金资助:
国家自然科学基金(32002061); 国家级大学生创新创业训练计划项目(202010879108); 安徽省蔬菜产业技术体系专项经费资助项目(皖农科函（2021）711号); 安徽省农业科学院青年英才经费资助项目(QNYC-201906); 安徽科技学院人才引进项目(NXYJ202103)

Genome-Wide Identification and Expression Analysis of DIR Gene Family in Cucumber

ZHANG KaiJing¹(), HE ShuaiShuai¹, JIA Li², HU YuChao¹, YANG DeKun¹, LU XiaoMin¹, ZHANG QiAn², YAN CongSheng²()

¹College of Agriculture, Anhui Science and Technology University, Fengyang 233100, Anhui
²Institute of Horticulture, Anhui Academy of Agricultural Sciences/Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province)/Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Anhui Province, Hefei 230031

Received:2022-04-13 Accepted:2022-06-07 Published:2023-02-16 Online:2023-02-24

摘要/Abstract

摘要：

【目的】基于黄瓜基因组信息和转录组测序大数据，利用生物信息学手段，对黄瓜中DIR基因家族进行鉴定，并分析其在不同组织器官和胁迫响应过程中的表达模式，为后续深入研究黄瓜DIR基因的生物学功能奠定重要基础。【方法】基于已报道的DIR基因HMM模型文件，利用HMMER软件包的hmmsearch程序从黄瓜蛋白数据库中筛选出可能的DIR基因ID，并利用在线工具Pfam和SMART进行验证，最终确定黄瓜DIR家族基因。利用ExPASy、TBtools、GSDS、MEME、MEGA、MCScanX和Circos等工具分析黄瓜DIR基因家族成员的理化特征、染色体定位、基因结构、系统进化树和共线性。基于黄瓜在不同组织和胁迫响应下的转录组测序大数据，利用黄瓜V3版本基因组信息进行转录组分析，检索黄瓜DIR基因在不同转录组测序分析中的表达情况，利用TBtools软件绘制表达热图，分析黄瓜DIR基因在不同组织和胁迫响应过程中的表达模式。【结果】在黄瓜中鉴定到23个DIR家族基因，分布于7条染色体上，编码氨基酸个数在78—684，分子量8.70—73.82 kD；系统进化分析将黄瓜DIR基因家族划分为3个亚族，每个亚族中的基因结构和motif基本一致；共线性分析发现黄瓜中有12个DIR基因与拟南芥中的19个DIR基因存在27种线性关系，黄瓜中有12个DIR基因与水稻中的11个DIR基因存在19种线性关系，而黄瓜中另外8个DIR基因比较保守，既不与拟南芥中的DIR基因存在共线性，也不与水稻中的DIR基因存在共线性；组织特异性表达分析发现有些黄瓜DIR基因在根、茎、花、果实、叶片等所有组织器官中的表达量均较低或不表达，有些黄瓜DIR基因在所有组织器官中的表达量均较高，而有些黄瓜DIR基因只在特定组织中表达，但在其他组织中不表达或低表达，表明不同的黄瓜DIR基因具有组织特异性表达模式；黄瓜DIR家族基因在胁迫响应过程中的表达模式分析发现CsaV3_4G023490在黄瓜非生物胁迫和生物胁迫响应过程中均发生上调表达，表明该基因在黄瓜生长发育过程中发挥着重要作用。【结论】在黄瓜中共鉴定到23个DIR家族基因，分为3个亚族，每个亚族内的基因成员保守性高，不同亚族间的基因结构和蛋白保守结构域有所不同。黄瓜DIR基因在不同组织器官和胁迫响应下的表达模式具有差异性，协同调控了黄瓜的生长发育。

关键词: 黄瓜, DIR, 基因家族, 生物信息学, 表达分析

Abstract:

【Objective】 Based on the cucumber (Cucumis sativus L.) genome information and transcriptome sequencing big-data, the DIR gene family in cucumber was identified with bioinformatics methods, and the expression pattern analysis of DIR family genes in different tissues and stresses response were analyzed. It would lay an important foundation for further study on the biological function of cucumber DIR genes. 【Method】 With the reported HMM model file of DIR gene, the probable DIR genes ID from the cucumber protein database was firstly identified using HMMSearch program in the HMMER software package. The cucumber DIR genes were ultimately verified using online tools Pfam and SMART. The tools of ExPASy, TBtools, GSDS, MEME, MEGA, MCScanX and Circos were used to analyze the physicochemical characteristics, chromosomal distributions, gene structure, phylogenetic tree and synteny of cucumber DIR genes. Based on cucumber transcriptome sequencing big-data of different tissues and under different stresses, transcriptome sequencing analysis was re-analyzed using cucumber V3 version genome information. The data of cucumber DIR genes in different transcriptome sequencing analysis were retrieved. The expression heatmaps of DIR gene family were drawn using TBtools software, and the expression patterns of cucumber DIR genes in different tissues and stresses response were analyzed. 【Result】 Total of 23 DIR genes were identified from cucumber genome, which distributed to 7 chromosomes. The number of amino acids of these DIR genes ranged from 78 to 684, and the molecular weight ranged from 8.70 to 73.82 kD. Phylogenetic analysis divided the cucumber DIR genes into 3 subgroups, the structure and motif of the genes in each subgroup were similar. Synteny analysis showed that the 12 cucumber DIR genes were collinearity with 19 Arabidopsis DIR genes and with 27 kinds of linear relationships, and 12 cucumber DIR genes were collinearity and with 11 rice DIR genes with 19 kinds of linear relationships. While only 8 cucumber DIR genes were conservative, which were not collinearity with any DIR gene in Arabidopsis and rice. Tissue-specific expression analysis revealed that some cucumber DIR genes had low or no expression levels in all tissues including root, stem, flower, fruit, leaf and so on, some cucumber DIR genes had high expression levels in all tissues, and some DIR genes had specific expression levels in some tissues, but no or low expression levels in other tissues. This suggested that different cucumber DIR genes had tissue specific expression patterns. The expression profiles analysis of cucumber DIR genes under biotic and abiotic stresses conditions revealed that cucumber DIR gene, CsaV3_4G023490, were up-regulated expression in response to all stresses, which meant this gene played an important role in the process of cucumber growth and development. 【Conclusion】 Total of 23 DIR genes were identified in cucumber, which were divided into 3 subgroups. The gene members in each subgroup were highly conserved, and the gene structure and protein conserved domain were different among 3 subgroups. The expression patterns of cucumber DIR genes in different tissues and stresses response were different, which coordinately regulated the growth and development of cucumber.

Key words: cucumber, DIR, gene family, bioinformatics, expression analysis

张开京, 何帅帅, 贾利, 胡玉超, 杨德坤, 陆晓民, 张其安, 严从生. 黄瓜DIR家族基因的全基因组鉴定及其表达分析[J]. 中国农业科学, 2023, 56(4): 711-728.

ZHANG KaiJing, HE ShuaiShuai, JIA Li, HU YuChao, YANG DeKun, LU XiaoMin, ZHANG QiAn, YAN CongSheng. Genome-Wide Identification and Expression Analysis of DIR Gene Family in Cucumber[J]. Scientia Agricultura Sinica, 2023, 56(4): 711-728.

图/表 11

表1

黄瓜23个DIR基因家族成员的理化特征"

基因 ID Gene ID	CDS大小 CDS size (bp)	氨基酸数目 Number of amino acids (aa)	分子量 Molecular weight (kD)	等电点 pI	不稳定性系数 Instability index	脂肪系数 Aliphatic index	亲水性平均值 Grand average of hydropathicity	亚细胞定位预测 Prediction of subcellular location
CsaV3_1G003340.1	552	183	19.94	6.06	32.24	90.00	0.255	质膜 Plasma membrane
CsaV3_1G003540.1	633	210	22.89	9.30	54.28	82.19	-0.111	线粒体 Mitochondrion
CsaV3_1G010290.1	774	257	27.81	5.69	46.08	75.53	-0.284	质膜Plasma membrane
CsaV3_2G015820.1	2055	684	73.82	9.13	33.65	92.27	-0.027	叶绿体 Chloroplast
CsaV3_2G015830.1	867	288	32.11	10.08	52.35	89.65	-0.136	质膜Plasma membrane
CsaV3_2G034820.1	639	212	22.68	9.69	21.78	78.73	-0.116	细胞外间隙 Extracellular space
CsaV3_3G011390.1	750	249	25.45	5.35	32.07	90.88	0.248	质膜Plasma membrane
CsaV3_3G015180.1	465	154	16.95	4.66	23.21	80.91	0.049	细胞外间隙 Extracellular space
CsaV3_4G006220.1	720	239	26.49	7.77	29.99	96.69	0.274	质膜Plasma membrane
CsaV3_4G006240.1	780	259	28.92	9.65	30.21	84.79	-0.055	质膜Plasma membrane
CsaV3_4G006250.1	576	191	21.26	8.63	28.03	86.81	0.163	质膜Plasma membrane
CsaV3_4G023480.1	237	78	8.70	9.85	36.49	70.00	-0.338	线粒体 Mitochondrion
CsaV3_4G023490.1	1284	427	48.16	9.48	35.62	88.85	-0.053	质膜Plasma membrane
CsaV3_4G023500.1	588	195	21.70	9.76	28.73	81.54	-0.030	质膜Plasma membrane
CsaV3_4G023510.1	528	175	19.53	9.58	23.03	95.20	-0.003	线粒体 Mitochondrion
CsaV3_5G006660.1	834	277	31.22	9.75	36.00	64.37	-0.420	线粒体 Mitochondrion
CsaV3_5G006670.1	1185	394	41.43	4.31	47.97	77.54	-0.177	细胞外间隙 Extracellular space
CsaV3_5G026130.1	990	329	34.01	5.08	33.90	79.12	-0.011	细胞外间隙 Extracellular space
CsaV3_6G006930.1	675	224	25.28	6.97	37.75	100.63	0.099	质膜Plasma membrane
CsaV3_7G003510.1	615	204	22.55	7.72	33.85	96.62	0.119	质膜Plasma membrane
CsaV3_7G005610.1	597	198	21.23	9.56	43.93	91.67	0.228	质膜Plasma membrane
CsaV3_7G005630.1	525	174	19.04	9.69	56.27	83.56	0.068	质膜Plasma membrane
CsaV3_7G022920.1	1770	589	66.23	8.49	49.45	89.63	-0.177	质膜Plasma membrane

表1

图1

图2

图3

表2

图4

图5

图6

图7

图8

图9

参考文献 59

[1]	BURLAT V, KWON M, DAVIN L B, LEWIS N G. Dirigent proteins and dirigent sites in lignifying tissues. Phytochemistry, 2001, 57(6): 883-897. doi: 10.1016/s0031-9422(01)00117-0 pmid: 11423139
[2]	EFFENBERGER I, HARPORT M, PFANNSTIEL J, KLAIBER I, SCHALLER A. Expression in Pichia pastoris and characterization of two novel dirigent proteins for atropselective formation of gossypol. Applied Microbiology and Biotechnology, 2017, 101(5): 2021-2032. doi: 10.1007/s00253-016-7997-3
[3]	HUANG S W, LI R Q, ZHANG Z H, LI L, GU X F, FAN W, LUCAS W J, WANG X W, XIE B Y, NI P X, REN Y, ZHU H M, LI J, LIN K, JIN W W, FEI Z J, LI G C, STAUB J B, KILIAN A, VAN DER VOSSEN E A G, et al. The genome of the cucumber, Cucumis sativus L. Nature Genetics, 2009, 41(12): 1275-1281.
[4]	陈家璐, 张智俊, 刘笑雨, 朱丰晓. 毛竹Dirigent基因家族的全基因组鉴定与分析. 植物生理学报, 2019, 55(9): 1406-1417. doi: 10.13592/j.cnki.ppj.2019.0238. doi: 10.13592/j.cnki.ppj.2019.0238.
	CHEN J L, ZHANG Z J, LIU X Y, ZHU F X. Genome-wide identification and analysis of Dirigent gene family in moso bamboo (Phyllostachys edulis). Plant Physiology Journal, 2019, 55(9): 1406-1417. doi: 10.13592/j.cnki.ppj.2019.0238. (in Chinese) doi: 10.13592/j.cnki.ppj.2019.0238.
[5]	RALPH S G, JANCSIK S, BOHLMANN J. Dirigent proteins in conifer defense II: Extended gene discovery, phylogeny, and constitutive and stress-induced gene expression in spruce (Picea spp.). Phytochemistry, 2007, 68(14): 1975-1991. doi: 10.1016/j.phytochem.2007.04.042
[6]	DAVIN L B, LEWIS N G. Dirigent phenoxy radical coupling: advances and challenges. Current Opinion in Biotechnology, 2005, 16(4): 398-406. pmid: 16023845
[7]	MA Q H, LIU Y C. TaDIR13, a dirigent protein from wheat, promotes lignan biosynthesis and enhances pathogen resistance. Plant Molecular Biology Reporter, 2014, 33: 143-152. doi: 10.1007/s11105-014-0737-x
[8]	DAVIN L B, WANG H B, CROWELL A L, BEDGAR D L, MARTIN D M, SARKANEN S, LEWIS N G. Stereoselective bimolecular phenoxy radical coupling by an auxiliary (dirigent) protein without an active center. Science, 1997, 275(5298): 362-366. doi: 10.1126/science.275.5298.362 pmid: 8994027
[9]	PANIAGUA C, BILKOVA A, JACKSON P, DABRAVOLSKI S, RIBER W, DIDI V, HOUSER J, GIGLI-BISCEGLIA N, WIMMEROVA M, BUDÍNSKÁ E, HAMANN T, HEJATKO J. Dirigent proteins in plants: Modulating cell wall metabolism during abiotic and biotic stress exposure. Journal of experimental botany, 2017, 68(13): 3287-3301. doi: 10.1093/jxb/erx141. doi: 10.1093/jxb/erx141 pmid: 28472349
[10]	LIAO Y R, LIU S B, JIANG Y Y, HU C Q, ZHANG X W, CAO X F, XU Z J, GAO X L, LI L H, ZHU J Q, CHEN R J. Genome-wide analysis and environmental response profiling of dirigent family genes in rice (Oryza sativa). Genes & Genomics, 2017, 39: 47-62.
[11]	SINGH D K, MEHRA S, CHATTERJEE S, PURTY R S. In silico identification and validation of miRNA and their DIR specific targets in Oryza sativa Indica under abiotic stress. Non-coding RNA Research, 2020, 5(4): 167-177. doi: 10.1016/j.ncrna.2020.09.002
[12]	CHENG X, SU X Q, MUHAMMAD A, LI M L, ZHANG J Y, SUN Y M, LI G H, JIN Q, CAI Y P, LIN Y. Molecular characterization, evolution, and expression profiling of the Dirigent (DIR) family genes in Chinese white pear (Pyrus bretschneideri). Frontiers in Genetics, 2018, 9: 136. doi: 10.3389/fgene.2018.00136
[13]	LI L L, SUN W B, ZHOU P J, WEI H, WANG P, LI H Y, REHMAN S, LI D W, ZHUGE Q. Genome-wide characterization of dirigent proteins in Populus: Gene expression variation and expression pattern in response to Marssonina brunnea and phytohormones. Forests, 2021, 12(4): 507. doi: 10.3390/f12040507
[14]	ARASAN S K T, PARK J I, AHMED N U, JUNG H J, HUR Y, KANG K K, LIM Y P, NOU I S. Characterization and expression analysis of dirigent family genes related to stresses in Brassica. Plant Physiology and Biochemistry, 2013, 67: 144-153. doi: 10.1016/j.plaphy.2013.02.030
[15]	KHAN A, LI R J, SUN J T, MA F, ZHANG H X, JIN J H, ALI M, HAQ S U, WANG J E, GONG Z H. Genome-wide analysis of dirigent gene family in pepper (Capsicum annuum L.) and characterization of CaDIR7 in biotic and abiotic stresses. Scientific Reports, 2018, 8: 5500. doi: 10.1038/s41598-018-23761-0
[16]	SHI Y Q, SHEN Y R, AHMAD B, YAO L P, HE T N, FAN J S, LIU Y H, CHEN Q X, WEN Z F. Genome-wide identification and expression analysis of dirigent gene family in strawberry (Fragaria vesca) and functional characterization of FvDIR13. Scientia Horticulturae, 2022, 297: 110913. doi: 10.1016/j.scienta.2022.110913
[17]	郭宝生, 师恭曜, 王凯辉, 刘素恩, 赵存鹏, 王兆晓, 耿军义, 华金平. 黄萎病菌侵染下陆地棉Dirigent-like蛋白基因表达差异分析. 中国农业科学, 2014, 47(22): 4349-4359. doi: 10.3864/j.issn.0578-1752.2014.22.001. doi: 10.3864/j.issn.0578-1752.2014.22.001.
	GUO B S, SHI G Y, WANG K H, LIU S E, ZHAO C P, WANG Z X, GENG J Y, HUA J P. Expression differences of dirigent-like protein genes in upland cotton respond to infection by Verticillium dahliae. Scientia Agricultura Sinica, 2014, 47(22): 4349-4359. doi: 10.3864/j.issn.0578-1752.2014.22.001. (in Chinese) doi: 10.3864/ j.issn.0578-1752.2014.22.001.
[18]	WU R H, WANG L L, WANG Z, SHANG H H, LIU X, ZHU Y, QI D D, DENG X. Cloning and expression analysis of a dirigent protein gene from the resurrection plant Boea hygrometrica. Progress in Natural Science, 2009, 19(3): 347-352. doi: 10.1016/j.pnsc.2008.07.010
[19]	GUO J L, XU L P, FANG J P, SU Y C, FU H Y, QUE Y X, XU J S. A novel dirigent protein gene with highly stem-specificexpression from sugarcane, response to drought, salt and oxidative stresses. Plant Cell Reports, 2012, 31(10): 1801-1812. doi: 10.1007/s00299-012-1293-1
[20]	ANDRADE L M, PEIXOTO-JUNIOR R F, RIBEIRO R V, NÓBILE P M, BRITO M S, MARCHIORI P E R, CARLIN S D, MARTINS A P B, GOLDMAN M H S, LLERENA J P P, FREGONESI C, PERECIN D, NEBÓ J F C D O, FIGUEIRA A, BENATTI T R, DA SILVA J, MAZZAFERA P, CRESTE S. Biomass accumulation and cell wall structure of rice plants overexpressing a dirigent-jacalin of sugarcane (ShDJ) under varying conditions of water availability. Frontiers in Plant Science, 2019, 10: 65. doi: 10.3389/fpls.2019.00065
[21]	LIU C H, QIN Z W, ZHOU X Y, XIN M, WANG C H, LIU D, LI S N. Expression and functional analysis of the propamocarb-related gene CsDIR16 in cucumbers. BMC Plant Biology, 2018, 18: 16. doi: 10.1186/s12870-018-1236-2
[22]	RALPH S, PARK J Y, BOHLMANN J, MANSFIELD S D. Dirigent proteins in conifer defense: Gene discovery, phylogeny, and differential wound- and insect-induced expression of a family of DIR and DIR-like genes in spruce (Picea spp.). Plant Molecular Biology, 2006, 60: 21-40. doi: 10.1007/s11103-005-2226-y
[23]	LI N H, ZHAO M, LIU T F, DONG L D, CHENG Q, WU J J, WANG L, CHEN X, ZHANG C Z, LU W C, XU P F, ZHANG S Z. A novel soybean dirigent gene GmDIR22 contributes to promotion of lignan biosynthesis and enhances resistance to Phytophthora sojae. Frontiers in Plant Science, 2017, 8: 1185. doi: 10.3389/fpls.2017.01185
[24]	SENEVIRATNE H K, DALISAY D S, KIM K W, MOINUDDIN S G A, YANG H, HARTSHORN C M, DAVIN L B, LEWIS N G. Non-host disease resistance response in pea (Pisum sativum) pods: Biochemical function of DRR206 and phytoalexin pathway localization. Phytochemistry, 2015, 13: 140-148.
[25]	REBOLEDO G, DEL CAMPO R, ALVAREZ A, MONTESANO M, MARA H, PONCE DE LEÓN I. Physcomitrella patens activates defense responses against the pathogen Colletotrichum gloeosporioides. International Journal of Molecular Sciences, 2015, 16(9): 22280-22298. doi: 10.3390/ijms160922280
[26]	BORGES A F, FERREIRA R B, MONTEIRO S. Transcriptomic changes following the compatible interaction Vitis vinifera-Erysiphe necator. Paving the way towards an enantioselective role in plant defence modulation. Plant Physiology and Biochemistry, 2013, 68: 71-80. doi: 10.1016/j.plaphy.2013.03.024
[27]	LING J, JIANG W J, ZHANG Y, YU H J, MAO Z C, GU X F, HUANG S W, XIE B Y. Genome-wide analysis of WRKY gene family in Cucumis sativus. BMC Genomics, 2011, 12: 471. doi: 10.1186/1471-2164-12-471
[28]	HU L F, LIU S Q. Genome-wide analysis of the MADS-box gene family in cucumber. Genome, 2012, 55(3): 245-256. doi: 10.1139/g2012-009 pmid: 22376137
[29]	WAN H, YUAN W, BO K, SHEN J, PANG X, CHEN J F. Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops. BMC Genomics, 2013, 14: 109. doi: 10.1186/1471-2164-14-109 pmid: 23418910
[30]	BALOGLU M C, ELDEM V, HAJYZADEH M, UNVER T. Genome-wide analysis of the bZIP transcription factors in cucumber. PLoS ONE, 2014, 9(4): e96014. doi: 10.1371/journal.pone.0096014
[31]	YADAV V, WANG Z Y, YANG X Z, WEI C H, CHANGQING X, ZHANG X. Comparative analysis, characterization and evolutionary study of dirigent gene family in cucurbitaceae and expression of novel dirigent peptide against powdery mildew stress. Genes, 2021, 12(3): 326. doi: 10.3390/genes12030326
[32]	LI Q, LI H B, HUANG W, XU Y C, ZHOU Q, WANG S H, RUAN J, HUANG S W, ZHANG Z H. A chromosome-scale genome assembly of cucumber (Cucumis sativus L.). GigaScience, 2019, 8(6): giz072. doi: 10.1093/gigascience/giz072. doi: 10.1093/gigascience/giz072.
[33]	MISTRY J, CHUGURANSKY S, WILLIAMS L, QURESHI M, SALAZAR G A, SONNHAMMER E L L, TOSATTO S C E, PALADIN L, RAJ S, RICHARDSON L J, FINN R D, BATEMAN A. Pfam: The protein families database in 2021. Nucleic Acids Research, 2021, 49(D1): D412-D419. doi: 10.1093/nar/gkaa913. doi: 10.1093/nar/gkaa913 pmid: 33125078
[34]	FINN R D, CLEMENTS J, EDDY S R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Research, 2011, 39: W29-W37. doi: 10.1093/nar/gkr367. doi: 10.1093/nar/gkr367.
[35]	LETUNIC I, KHEDKAR S, BORK P. SMART: Recent updates, new developments and status in 2020. Nucleic Acids Research, 2021, 49(D1): D458-D460. doi: 10.1093/nar/gkaa937. doi: 10.1093/nar/gkaa937 pmid: 33104802
[36]	YU C S, LIN C J, HWANG J K. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Science, 2004, 13(5): 1402-1406. doi: 10.1110/ps.03479604
[37]	CHEN C J, CHEN H, ZHANG Y, THOMAS H R, FRANK M H, HE Y H, XIA R. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 2020, 13(8): 1194-1202. doi: S1674-2052(20)30187-8 pmid: 32585190
[38]	HU B, JIN J P, GUO A Y, ZHANG H, LUO J C, GAO G. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics, 2015, 31(8): 1296-1297. doi: 10.1093/bioinformatics/btu817. doi: 10.1093/bioinformatics/btu817 pmid: 25504850
[39]	BAILEY T L, WILLIAMS N, MISLEH C, LI W W. MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research, 2006, 34: W369-W373. doi: 10.1093/nar/gkl198. doi: 10.1093/nar/gkl198 pmid: 16845028
[40]	TAMURA K, STECHER G, KUMAR S. MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 2021, 38(7): 3022-3027. doi: 10.1093/molbev/msab120. doi: 10.1093/molbev/msab120 pmid: 33892491
[41]	LESCOT M, DÉHAIS P, THIJS G, MARCHAL K, MOREAU Y, VAN DE PEER Y, ROUZÉ P, ROMBAUTS S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 2002, 30(1): 325-327. doi: 10.1093/nar/30.1.325. doi: 10.1093/nar/30.1.325 pmid: 11752327
[42]	WANG Y P, TANG H B, DEBARRY J D, TAN X, LI J P, WANG X Y, LEE T H, JIN H Z, MARLER B, GUO H, KISSINGER J C, PATERSON A H. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 2012, 40(7): e49. doi: 10.1093/nar/gkr1293. doi: 10.1093/nar/gkr1293.
[43]	KRZYWINSKI M, SCHEIN J, BIROL I, CONNORS J, GASCOYNE R, HORSMAN D, JONES S J, MARRA M A. Circos: An information aesthetic for comparative genomics. Genome Research, 2009, 19(9): 1639-1645. doi: 10.1101/gr.092759.109 pmid: 19541911
[44]	LI Z, ZHANG Z H, YAN P C, HUANG S W, FEI Z J, LIN K. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 2011, 12: 540. doi: 10.1186/1471-2164-12-540 pmid: 22047402
[45]	CHEN C H, CHEN X Q, HAN J, LU W L, REN Z H. Genome-wide analysis of the WRKY gene family in the cucumber genome and transcriptome-wide identification of WRKY transcription factors that respond to biotic and abiotic stresses. BMC Plant Biology, 2020, 20: 443. doi: 10.1186/s12870-020-02625-8
[46]	ZHU Y X, YIN J L, LIANG Y F, LIU J Q, JIA J H, HUO H Q, WU Z F, YANG R L, GONG H J. Transcriptomic dynamics provide an insight into the mechanism for silicon-mediated alleviation of salt stress in cucumber plants. Ecotoxicology and Environmental Safety, 2019, 174: 245-254. doi: S0147-6513(19)30234-9 pmid: 30831473
[47]	BURKHARDT A, DAY B. Transcriptome and small RNAome dynamics during a resistant and susceptible interaction between cucumber and downy mildew. Plant Genome, 2016, 9(1): 1-19.
[48]	XU Q, XU X X, SHI Y, QI X H, CHEN X H. Elucidation of the molecular responses of a cucumber segment substitution line carrying Pm5.1 and its recurrent parent triggered by powdery mildew by comparative transcriptome profiling. BMC Genomics, 2017, 18: 21. doi: 10.1186/s12864-016-3438-z
[49]	WANG X, CHENG C Y, ZHANG K J, TIAN Z, XU J, YANG S Q, LOU Q F, LI J, CHEN J F. Comparative transcriptomics reveals suppressed expression of genes related to auxin and the cell cycle contributes to the resistance of cucumber against Meloidogyne incognita. BMC Genomics, 2018, 19: 583. doi: 10.1186/s12864-018-4979-0
[50]	谢玲娟, 叶楚玉, 沈恩惠. 植物基因组测序研究进展. 植物科学学报, 2021, 39(6): 681-691. doi: 10.11913/PSJ.2095-0837.2021.60681. doi: 10.11913/PSJ.2095-0837.2021.60681.
	XIE L J, YE C Y, SHEN E H. Advances in plant genome construction. Plant Science Journal, 2021, 39(6): 681-691. doi: 10.11913/PSJ.2095-0837.2021.60681. (in Chinese) doi: 10.11913/PSJ.2095-0837.2021.60681.
[51]	UN Food and Agriculture Organization,Corporate Statistical Database (FAOSTAT). Production of cucumbers and gherkins in 2016[OL], 2017.
[52]	JAIN M, TYAGI A K, KHURANA J P. Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa). Genomics, 2006, 88(3): 360-371. doi: 10.1016/j.ygeno.2006.04.008 pmid: 16707243
[53]	ZHANG S B, CHEN C, LI L, MENG L, SINGH J, JIANG N, DENG X W, HE Z H, LEMAUX P G. Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family. Plant Physiology, 2005, 139(3): 1107-1124. doi: 10.1104/pp.105.069005. doi: 10.1104/pp.105.069005. pmid: 16286450
[54]	崔凯, 吴伟伟, 刁其玉. 转录组测序技术的研究和应用进展. 生物技术通报, 2019, 35(7): 1-9. doi: 10.13560/j.cnki.biotech.bull.1985.2019-0374. doi: 10.13560/j.cnki.biotech.bull.1985.2019-0374
	CUI K, WU W W, DIAO Q Y. Application and research progress on transcriptomics. Biotechnology Bulletin, 2019, 35(7): 1-9. doi: 10.13560/j.cnki.biotech.bull.1985.2019-0374. (in Chinese) doi: 10.13560/j.cnki.biotech.bull.1985.2019-0374
[55]	LIU Q Q, LUO L, ZHENG L Q. Lignins: Biosynthesis and biological functions in plants. International Journal of Molecular Sciences, 2018, 19(2): 335. doi: 10.3390/ijms19020335
[56]	ALVAREZ A, MONTESANO M, SCHMELZ E, PONCE DE LEÓN I. Activation of shikimate, phenylpropanoid, oxylipins, and auxin pathways in Pectobacterium carotovorum elicitors-treated moss. Frontiers in Plant Science, 2016, 7: 328.
[57]	PONCE DE LEÓN I, SCHMELZ E A, GAGGERO C, CASTRO A, ÁLVAREZ A, MONTESANO M. Physcomitrella patens activates reinforcement of the cell wall, programmed cell death and accumulation of evolutionary conserved defence signals, such as salicylic acid and 12-oxo-phytodienoic acid, but not jasmonic acid, upon Botrytis cinerea infection. Molecular Plant Pathology, 2012, 13(8): 960-974. doi: 10.1111/j.1364-3703.2012.00806.x
[58]	WEIDENBACH D, ESCH L, MÖLLER C, HENSEL G, KUMLEHN J, HÖFLE C, HÜCKELHOVEN R, SCHAFFRATH U. Polarized defense against fungal pathogens is mediated by the jacalin-related lectin domain of modular poaceae-specific proteins. Molecular Plant, 2016, 9(4): 514-527. doi: 10.1016/j.molp.2015.12.009
[59]	CORBIN C, DROUET S, MARKULIN L, AUGUIN D, LAINÉ É, DAVIN L B, CORT J R, LEWIS N G, HANO C. A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: From gene identification and evolution to differential regulation. Plant Molecular Biology, 2018, 97: 73-101. doi: 10.1007/s11103-018-0725-x

基序 Motif	序列 Sequence	氨基酸数目 Number of amino acid	Pfam注释 Pfam annotation
motif 1	FGTVVVIDBPLTEGPELGSKLIGRAQGFYASASQDGFGLLM	41	Dirigent
motif 2	JSFFGRNPILEKVREMPVVGGTGKFRFARG	30	Dirigent
motif 3	THLRFYFHDILSGKNPTAIAV	21	Dirigent
motif 4	AMNFAFTSGKYNGSS	15	Dirigent
motif 5	YAKAKTHYLDFTTGDAVVEYN	21	-
motif 6	EDENSFARTVNRKRLGLRKEK	21	-
motif 7	TITVLALFLFSSSSCSALPMVKKQKHKPC	29	-
motif 8	VPPVSNTSRTR	11	-
motif 9	MAGISPISPTHFLFLSFLL	19	-
motif 10	ENQHVTDGVDTJJHFSVYLSY	21	-

黄瓜DIR家族基因的全基因组鉴定及其表达分析

Genome-Wide Identification and Expression Analysis of DIR Gene Family in Cucumber

RichHTML

PDF

赞

可视化

摘要/Abstract

引用本文

使用本文

图/表 11

参考文献 59

相关文章 15

Metrics

本文评价

推荐阅读 0

[1]	曹海顺, 周东源, 王瑞, 施招婉, 吴廷全, 张长远. 弱光胁迫短下胚轴黄瓜种质鉴定及其遗传位点挖掘[J]. 中国农业科学, 2026, 59(6): 1286-1301.
[2]	张利东, 郭一聪, 黄洪宇, 聂静, 王兵, 李梦雨, 李加旺, 眭晓蕾, 李愚鹤. 基于感官评价结合营养品质特征与风味物质特性关联分析黄瓜果实品质[J]. 中国农业科学, 2026, 59(5): 1087-1100.
[3]	罗正英, 胡嗣桢, 林秀琴, 胡鑫, 张敏, 徐超华, 刘新龙, 曾千春. 甘蔗属割手密与热带种PEBP基因家族的鉴定及其开花调控功能分析[J]. 中国农业科学, 2026, 59(4): 734-749.
[4]	江峰, 吴春燕, 王亦好, 杨泽众, 龚成, 罗晨. 烟粉虱MED脂肪酸延长酶基因家族鉴定和表达分析[J]. 中国农业科学, 2026, 59(4): 793-806.
[5]	付涵, 于杨, 艾妞, 张思晴, 于连伟, 孙书豪, 赵金章, 韩晓玉, 施艳, 杨雪. 光合作用系统Ⅱ相关蛋白NbPsbQ1通过促进光合效率抑制病毒侵染[J]. 中国农业科学, 2026, 59(1): 90-100.
[6]	杨彩丽, 李永洲, 贺亮亮, 宋银花, 章鹏, 刘肇先, 李鹏慧, 刘三军. 葡萄TPS基因家族全基因组鉴定及VvTPS4在单萜形成中的功能验证[J]. 中国农业科学, 2025, 58(7): 1397-1417.
[7]	滕梦鑫, 徐亚, 何静, 汪奇, 乔飞, 李敬阳, 李新国. 香蕉Ca²⁺-ATPase基因家族的鉴定及功能分析[J]. 中国农业科学, 2025, 58(7): 1418-1433.
[8]	张天雨, 李白, 藏金萍, 曹宏哲, 董金皋, 邢继红, 张康. 灰葡萄孢HMG家族基因的全基因组鉴定与表达规律分析[J]. 中国农业科学, 2025, 58(4): 704-718.
[9]	李建昆, 彭超, 张子扬, 梁茜, 魏鸣康, 杨强, 李斌奇, Muhammad Moaaz Ali, Viola Kayima, 陈发兴, 邓红红. ‘皇冠’李果实空腔褐变与木质素积累的关系及其4CL基因家族鉴定[J]. 中国农业科学, 2025, 58(4): 759-778.
[10]	张林琳, 宫瑞, 崔彦玲, 钟雄辉, 李烨, 李然红, 潜宗伟. 利用VIGS分析SmWRKY30在茄子抗青枯病中的作用[J]. 中国农业科学, 2025, 58(3): 548-563.
[11]	仪泽会, 王颖, 宋慧霞, 赵婧, 毛丽萍. 芦笋过氧化物还原酶（Peroxiredoxins）基因家族全基因组鉴定及表达分析[J]. 中国农业科学, 2025, 58(18): 3728-3743.
[12]	齐香玉, 李新茹, 陈双双, 冯景, 陈慧杰, 刘欣童, 金玉妍, 邓衍明. 茉莉花FLA基因家族鉴定及JsFLA2的功能分析[J]. 中国农业科学, 2025, 58(17): 3516-3530.
[13]	廖锴, 李欣, 石延霞, 谢学文, 李磊, 范腾飞, 王绍辉, 李宝聚, 柴阿丽. 塑料拱棚不同通风方式对黄瓜细菌性角斑病传播的影响[J]. 中国农业科学, 2025, 58(10): 1934-1946.
[14]	王伟, 吴传磊, 胡晓渝, 李佳佳, 白鹏宇, 王郭伋, 苗龙, 王晓波. 大豆LOX基因家族的全基因组鉴定及GmLOX15A1基因等位变异对百粒重的影响[J]. 中国农业科学, 2025, 58(1): 10-29.
[15]	姜兴林, 于连伟, 付涵, 艾妞, 崔荧钧, 李好海, 夏子豪, 袁虹霞, 李洪连, 杨雪, 施艳. 转录因子NbMYB1R1通过促进活性氧积累抑制病毒侵染[J]. 中国农业科学, 2024, 57(8): 1490-1505.